Patrick R. O'neil Form 4 IONIS PHARMACEUTICALS / PATRICK R. O'NEIL ownership change

SEC Form 4

FORM 4

UNITED STATES SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

STATEMENT OF CHANGES IN BENEFICIAL OWNERSHIP

Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934
or Section 30(h) of the Investment Company Act of 1940

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Check this box if no longer subject to Section 16. Form 4 or Form 5 obligations may continue. See Instruction 1(b).

1. Name and Address of Reporting Person^*

O'NEIL PATRICK R.

(Last) (First) (Middle)

C/O IONIS PHARMACEUTICALS, INC.

2855 GAZELLE COURT

(Street)

CARLSBAD CA 92010

(City) (State) (Zip)

2. Issuer Name and Ticker or Trading Symbol
IONIS PHARMACEUTICALS INC [ IONS ]

5. Relationship of Reporting Person(s) to Issuer
(Check all applicable)

	Director	10% Owner
X	Officer (give title below)	Other (specify below)
SVP, Legal & General Counsel

3. Date of Earliest Transaction (Month/Day/Year)
11/14/2016

4. If Amendment, Date of Original Filed (Month/Day/Year)

6. Individual or Joint/Group Filing (Check Applicable Line)

X	Form filed by One Reporting Person
	Form filed by More than One Reporting Person

Table I - Non-Derivative Securities Acquired, Disposed of, or Beneficially Owned
1. Title of Security (Instr. 3)	2. Transaction Date (Month/Day/Year)	2A. Deemed Execution Date, if any (Month/Day/Year)	3. Transaction Code (Instr. 8)		4. Securities Acquired (A) or Disposed Of (D) (Instr. 3, 4 and 5)			5. Amount of Securities Beneficially Owned Following Reported Transaction(s) (Instr. 3 and 4)	6. Ownership Form: Direct (D) or Indirect (I) (Instr. 4)	7. Nature of Indirect Beneficial Ownership (Instr. 4)
			Code	V	Amount	(A) or (D)	Price
Common Stock	11/14/2016	11/14/2016	M(1)		194(1)	A	$10.82	9,720	D
Common Stock	11/14/2016	11/14/2016	S(1)		194(1)	D	$45	9,526	D
Common Stock	11/14/2016	11/14/2016	M(1)		806(1)	A	$10.82	10,332	D
Common Stock	11/14/2016	11/14/2016	S(1)		806(1)	D	$45	9,526	D

Table II - Derivative Securities Acquired, Disposed of, or Beneficially Owned (e.g., puts, calls, warrants, options, convertible securities)
1. Title of Derivative Security (Instr. 3)	2. Conversion or Exercise Price of Derivative Security	3. Transaction Date (Month/Day/Year)	3A. Deemed Execution Date, if any (Month/Day/Year)	4. Transaction Code (Instr. 8)		5. Number of Derivative Securities Acquired (A) or Disposed of (D) (Instr. 3, 4 and 5)		6. Date Exercisable and Expiration Date (Month/Day/Year)		7. Title and Amount of Securities Underlying Derivative Security (Instr. 3 and 4)		8. Price of Derivative Security (Instr. 5)	9. Number of derivative Securities Beneficially Owned Following Reported Transaction(s) (Instr. 4)	10. Ownership Form: Direct (D) or Indirect (I) (Instr. 4)	11. Nature of Indirect Beneficial Ownership (Instr. 4)
				Code	V	(A)	(D)	Date Exercisable	Expiration Date	Title	Amount or Number of Shares
Employee Stock Option (right to buy)	$10.82	11/14/2016	11/14/2016	M			194	01/02/2014(2)	01/01/2020	Common Stock	194	$0	4,907	D
Employee Stock Option (right to buy)	$10.82	11/14/2016	11/14/2016	M			806	01/02/2014(3)	01/01/2020	Common Stock	806	$0	2,694	D

Explanation of Responses:

1. Acquired as a result of exercising a stock option pursuant to Rule 10b5-1 Trading Plan. The purchase and sale reported on this Form 4 was effective pursuant to Rule 10b5-1 Trading Plan adopted by the reporting person on 9/21/2015.

2. Grant of 1/2/2013 to reporting person of stock options under the Ionis Pharmaceuticals, Inc. 1989 Stock Option Plan. 25% of the shares subject to the option vested and became exercisable on 1/2/2014. Thereafter, the remaining shares subject to the option vest and become exercisable in 36 equal monthly installments, at the rate of 3,925 shares per year. Following this transaction, the option was exercisable as to 4,252 on 11/14/2016.

3. Grant of 1/2/2013 to reporting person of stock options under the Ionis Pharmaceuticals, Inc. 1989 Stock Option Plan. 25% of the shares subject to the option vested and became exercisable on 1/2/2014. Thereafter, the remaining shares subject to the option vest and become exercisable in 36 equal monthly installments, at the rate of 1,875 shares per year. Following this transaction, the option was exercisable as to 2,381 on 11/14/2016.

Remarks:

	/s/Patrick R. O'Neil	11/14/2016
	** Signature of Reporting Person	Date
Reminder: Report on a separate line for each class of securities beneficially owned directly or indirectly.
* If the form is filed by more than one reporting person, see Instruction 4 (b)(v).
** Intentional misstatements or omissions of facts constitute Federal Criminal Violations See 18 U.S.C. 1001 and 15 U.S.C. 78ff(a).
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